Archive for the ‘Interesting chemistry’ Category
Sunday, February 17th, 2013
My last comment as appended to the previous post promised to analyse two so-called extended porphyrins for their topological descriptors. I start with the Cãlugãreanu/Fuller theorem which decomposes the topology of a space curve into two components, its twist (Tw) and its writhe (Wr, this latter being the extent to which coiling of the central curve has relieved local twisting) and establishes a topological invariant called the linking number[1]
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References
- S.M. Rappaport, and H.S. Rzepa, "Intrinsically Chiral Aromaticity. Rules Incorporating Linking Number, Twist, and Writhe for Higher-Twist Möbius Annulenes", Journal of the American Chemical Society, vol. 130, pp. 7613-7619, 2008. https://doi.org/10.1021/ja710438j
Tags:conjugated systems, helical systems
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Tuesday, February 12th, 2013
An extensive discussion developed regarding my post on a fascinating helical [144]-annulene. Topics included the nature of the ring current sustained by the π-electrons and in particular the bond-length alternation around the periphery and whether this should alter if the electron count were to be changed to that of a 4n+2 system (i.e. a dication). Whilst the [144]-annulene itself is hypothetical, it emerged that some compounds known as expanded porphyrins have very similar (albeit smaller scale) helical structures. X-ray structures for two such provide useful reality checks on the calculations. Here‡ I include the (3D) coordinates of these two systems so that you can explore for yourself their helicity.
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Tags:Helical annulenes, X-ray
Posted in Interesting chemistry | 13 Comments »
Monday, February 11th, 2013
This is really just a postscript to the previous post. There I showed how a search of the (small molecule) crystal database revealed the s-cis conformation about the N-C amide bond (the one with partial double bond character that prevents rotation) and how this conformation means that a C-H approaches quite closely to an adjacent oxygen. It is a tiny step from that search to a related, and very famous one named after Ramachandran[1]. Indeed this search, and the contour map used to display the results, really put crystal databases on the map so to speak.
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References
- G. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, "Stereochemistry of polypeptide chain configurations", Journal of Molecular Biology, vol. 7, pp. 95-99, 1963. https://doi.org/10.1016/s0022-2836(63)80023-6
Tags:conformational analysis, search above, Tutorial material
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Friday, February 8th, 2013
Consider acetaldehyde (ethanal for progressive nomenclaturists). What conformation does it adopt, and why? This question was posed of me by a student at the end of a recent lecture of mine. Surely, an easy answer to give? Read on …
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Tags:Cambridge, conformational analysis, energy, free energy, steric exchange energy, Tutorial material
Posted in crystal_structure_mining, Interesting chemistry | 1 Comment »
Sunday, February 3rd, 2013
The electronic interaction between a single bond and an adjacent double bond is often called σ-π-conjugation (an older term for this is hyperconjugation), and the effect is often used to e.g. explain why more highly substituted carbocations are more stable than less substituted ones. This conjugation is more subtle in neutral molecules, but following my use of crystal structures to explore the so-called gauche effect (which originates from σ-σ-conjugation), I thought I would have a go here at seeing what the crystallographic evidence actually is for the σ-π-type.
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Tags:above search, Cambridge, conformational analysis, Tutorial material, X-ray
Posted in crystal_structure_mining, Interesting chemistry | 1 Comment »
Friday, February 1st, 2013
This is a recently published[1] (hypothetical) molecule which has such unusual properties that I cannot resist sharing it with you. It is an annulene with 144 all-cis CH groups, being a (very) much larger cousin of (also hypothetical) systems mooted in 2009[2],[3].
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References
- R.J.F. Berger, "Prediction of a Cyclic Helical Oligoacetylene Showing Anapolar Ring Currents in the Magnetic Field", Zeitschrift für Naturforschung B, vol. 67, pp. 1127-1131, 2012. https://doi.org/10.5560/znb.2012-0189
- S.M. Rappaport, and H.S. Rzepa, "Intrinsically Chiral Aromaticity. Rules Incorporating Linking Number, Twist, and Writhe for Higher-Twist Möbius Annulenes", Journal of the American Chemical Society, vol. 130, pp. 7613-7619, 2008. https://doi.org/10.1021/ja710438j
- C.S. Wannere, H.S. Rzepa, B.C. Rinderspacher, A. Paul, C.S.M. Allan, H.F. Schaefer, and P.V.R. Schleyer, "The Geometry and Electronic Topology of Higher-Order Charged Möbius Annulenes", The Journal of Physical Chemistry A, vol. 113, pp. 11619-11629, 2009. https://doi.org/10.1021/jp902176a
Tags:helical metal wire, helical systems
Posted in Interesting chemistry | 56 Comments »
Friday, January 25th, 2013
Although have dealt with the π-complex formed by protonation of PhNHOPh in several posts, there was one aspect that I had not really answered; what is the most appropriate description of its electronic nature? Here I do not so much provide an answer, as try to show how difficult getting an accurate answer might be.
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Tags:electronic energy, energy, multi-reference solution
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Saturday, January 19th, 2013
The transient π-complex formed during the “[5,5]” sigmatropic rearrangement of protonated N,O-diphenyl hydroxylamine can be (formally) represented as below, namely the interaction of a six-π-electron aromatic ring (the phenoxide anion 2) with a four-π-electron phenyl dication-anion pair 1. Can one analyse this interaction in terms of aromaticity?
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Tags:chemical, Michael Dewar
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Friday, January 18th, 2013
Michael Dewar[1] famously implicated a so-called π-complex in the benzidine rearrangement, back in the days when quantum mechanical calculations could not yet provide a quantitatively accurate reality check. Because this π-complex actually remains a relatively unusual species to encounter in day-to-day chemistry, I thought I would try to show in a simple way how it forms.
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References
- M. Dewar, and H. McNicoll, "Mechanism of the benzidine rearrangement", Tetrahedron Letters, vol. 1, pp. 22-23, 1959. https://doi.org/10.1016/s0040-4039(01)82765-9
Tags:energy, high energy molecules, Michael Dewar, Reaction Mechanism
Posted in Interesting chemistry | 2 Comments »